Abstract

Copy number variations (CNVs) are major forms of genetic variation with an increasing importance in animal genomics. This study used the Illumina BovineSNP 50 K BeadChip to detect the genome-wide CNVs in the Tharparkar cattle. With the aid of PennCNV software, we noticed a total of 447 copy number variation regions (CNVRs) across the autosomal genome, occupying nearly 2.17% of the bovine genome. The average size of detected CNVRs was found to be 122.2 kb, the smallest CNVR being 50.02 kb in size, to the largest being 1,232.87 Kb. Enrichment analyses of the genes in these CNVRs gave significant associations with molecular adaptation-related Gene Ontology (GO) terms. Most CNVR genes were significantly enriched for specific biological functions; signaling pathways, sensory responses to stimuli, and various cellular processes. In addition, QTL analysis of CNVRs described them to be linked with economically essential traits in cattle. The findings here provide crucial information for constructing a more comprehensive CNVR map for the indigenous cattle genome.

摘要

拷贝数变异 (CNV) 是遗传变异的主要形式，在动物基因组学中的重要性日益增加。本研究使用 Illumina BovineSNP 50 K BeadChip 检测 Tharparkar 牛的全基因组 CNV。借助PennCNV软件，我们注意到整个常染色体基因组共有 447 个拷贝数变异区域 (CNVR)，占牛基因组的近 2.17%。发现检测到的 CNVR 的平均大小为 122.2 kb，最小的 CNVR 为 50.02 kb，最大的为 1,232.87 Kb。这些 CNVR 中基因的富集分析给出了与分子适应相关基因本体论 (GO) 术语的显着关联。大多数 CNVR 基因都显着丰富了特定的生物学功能；信号通路、对刺激的感觉反应和各种细胞过程。此外，CNVR 的 QTL 分析表明它们与牛的经济基本性状有关。这里的发现为构建更全面的本地牛基因组 CNVR 图谱提供了重要信息。